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The station signed-on November 27, 1978 as the market's fourth television outlet. The station first broadcast from studios located on Kishwaukee Street in Rockford. It was the last full-power analog television station to sign-on in Rockford while other stations in the area since then have either been low-powered, cable-only, or a digital subchannels. Airing an analog signal on UHF channel 39, WQRF was founded by local businessman Marvin Palmquist. The channel allotment was previously used by WTVO from its sign-on until 1967. It was promoted as an Independent, "family-oriented" alternative to the area's big three network affiliates. Palmquist sold the station to Orion Broadcasting in 1984.

The station joined Fox in August 1989 and, until that point, programming from the network was offered through Chicago's WFLD, Madison's WMSN-TV, or Milwaukee's WCGV (Fox affiliate at the time) depending on location. Within four years of joining Fox, WQRF ranked as one of the network's highest-rated stations. On September 12 of that year, Family Group sold the station to Petracom Broadcasting. Petracom in turn sold it to Quorum Broadcasting in 1998.

Of course with the expansion of Fox's primetime programming and due to the lack of a fifth commercial station in the market, much of WQRF's off-network reruns from yesteryear and sports coverage had gradually disappeared. The station joined Nexstar as part of the company's acquisition of Quorum Broadcasting in late-2003. On November 22, 2004, Mission Broadcasting bought WTVO from Young Broadcasting for $21 million, entered into a shared services agreement with WQRF, with WQRF moving into WTVO's studio.

WQRF-TV shut down its analog signal, over UHF channel 39, on February 17, 2009, the original target date in which full-power television stations in the United States were to transition from analog to digital broadcasts under federal mandate (which was later pushed back to June 12, 2009). The station's digital signal remained on its pre-transition UHF channel 42.[2] Through the use of PSIP, digital television receivers display the station's virtual channel as its former UHF analog channel 39.

In March 2006, WTVO began producing the market's second prime time newscast on WQRF known as Fox 39 News at 9. The broadcast only aired on weeknights unlike the area's original prime time show that was seen every night on cable-onlyWB affiliate "WBR" (produced by WREX). This distinction made WQRF's news Rockford's first over-the-air newscast at 9. Competition between "WBR" and WQRF was short lived because, in late-2007, the former had its news canceled by WREX for an unknown reason. The time slot is currently used to replay the NBC outlet's weeknight 6 o'clock show on what is now CW affiliate WREX-DT2.

Another addition to local newscasts on WQRF occurred January 14, 2008 when WTVO launched Fox 39 Evening News at 6:30. This broadcast was seen weeknights and aired against the national broadcasts on the area's big three affiliates. Eventually, WQRF expanded Fox 39 News at 9 to a seven night operation and lengthened the weeknight version to a full hour. This station would eventually drop the 6:30 show for an unknown reason. WQRF's weeknight prime time newscast at 9 maintains a separate news anchor but features the same meteorologist and sports anchor as WTVO.

On March 5, 2012, WTVO launched a two-hour-long extension of its weekday morning show on WQRF. Known as Fox 39 News in the Morning, this can be seen from 7 until 9 offering a local alternative to the national morning programs that air on the area's big three outlets. WIFR was the first television station in Rockford to upgrade its newscasts to high definition followed by WREX on December 12, 2010. On December 18, 2012, WTVO and WQRF debuted a brand new set, news music package, and graphics scheme that is based on the Eyewitness News branding seen on other Nexstar/Mission television stations. On April 24, 2013, WQRF began broadcasting local news content in high definition.